diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 9695428f3..95633c222 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -557,8 +557,11 @@ public class PairHMMIndelErrorModel {
                         long indStop =  stop - haplotype.getStartPosition();
 
                         double readLikelihood;
+                        if (DEBUG)
+                            System.out.format("indStart: %d indStop: %d WinStart:%d WinStop:%d start: %d stop: %d readLength: %d C:%s\n",
+                                    indStart, indStop, ref.getWindow().getStart(), ref.getWindow().getStop(), start, stop, read.getReadLength(), read.getCigar().toString());
 
-                        if (indStart < 0 || indStop >= haplotype.getBases().length) {
+                        if (indStart < 0 || indStop >= haplotype.getBasesAsBytes().length || indStart > indStop) {
                             // read spanned more than allowed reference context: we currently can't deal with this
                             readLikelihood =0;
                         } else